f2: ChIP-seq of HFSCs reveals genome-wide reduction of H3 K9/K27me3 in catagen.(a) Scheme of hair cycle stages that were used for ChIP-seq of this work (blue) and Lien et al. (* gray)23. (b) Representative FACS plot that shows the sorting scheme of HFSCs and non-HFSCs. (c) Total number of peaks called for all three marks using MACS24. Raw ChIP-seq signals from publically available databases (GEO accession: GSE31239) were employed in our analysis methods to generate peaks for the Lien et al.23 study that were directly comparable with our data. Note the reduction in the total peak number in LC-HFSCs (arrow), especially prominent for K9/K27me3. (d) Venn diagram of all genes present with one or more histone marks in their transcription start sites, within 3,000 bp upstream and downstream. Note that ∼90% of genes are commonly marked in the two studies that used independent ChIP-seq methods. (e) Genome view of MACS peaks from ChIP-seq data of this study and of the study by Lien et al.23. Chr, chromosome number. Note that large-scale enrichment patterns across the genome are similar between the two studies, as expected. H3K27me3 shows visible reduction in overall signal in LC-HFSCs. (f) Genome-wide view of H3K9me3 (K9) ChIP-seq peaks in different sorted populations. Chr, chromosome number. Notice a dramatic reduction in the overall signal in LC-HFSCs.

Mentions:
To examine genome-wide distribution and levels of DNA-bound methylated histone H3 K4/K9/K27me3, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq). We used comparable number of sorted CD34+/α6-integrin+ EA-HFSCs (PD22–25) and LC-HFSCs (PD38–44; Fig. 2a,b). We also sorted and analysed non-HFSCs (nEA and nLC) counterparts as CD34−/α6-integrin+. Using IgG as background for normalization, our data revealed good correlation between experiments and enrichments in specific functional genomic regions, such as promoters, introns and repetitive regions, as expected (Supplementary Fig. 2a,b). We compared our data with a previous ChIP-seq study of H3K4me3 and H3K27me3 (H3K9me3 was not analysed) by Lien et al.23, done at Mid/late Anagen (MA-HFSCs) and Late Telogen (LT-HFSCs; Fig. 2a–e). The overall genome-wide distribution for the marks was similar in the two studies (Fig. 2d,e), however, our data uniquely revealed fewer ChIP-seq peaks in LC-HFSCs when compared with EA-HFSCs (Fig. 2c and Supplementary Fig. 2c). Close examination of ChIP-seq data distribution across the genome showed that for H3K27me3 and especially for H3K9me3 not only the total number of peaks but also the height was dramatically decreased in LC-HFSCs (Fig. 2e,f, arrows). In case of H3K4me3, the number of peaks were marginally decreased in LC-HFSCs relative to the other populations (Fig. 2c,e), which prompted us to examine the ChIP-seq signals in a manner that would allow more quantitative examination of signal at discrete chromosomal loci.

f2: ChIP-seq of HFSCs reveals genome-wide reduction of H3 K9/K27me3 in catagen.(a) Scheme of hair cycle stages that were used for ChIP-seq of this work (blue) and Lien et al. (* gray)23. (b) Representative FACS plot that shows the sorting scheme of HFSCs and non-HFSCs. (c) Total number of peaks called for all three marks using MACS24. Raw ChIP-seq signals from publically available databases (GEO accession: GSE31239) were employed in our analysis methods to generate peaks for the Lien et al.23 study that were directly comparable with our data. Note the reduction in the total peak number in LC-HFSCs (arrow), especially prominent for K9/K27me3. (d) Venn diagram of all genes present with one or more histone marks in their transcription start sites, within 3,000 bp upstream and downstream. Note that ∼90% of genes are commonly marked in the two studies that used independent ChIP-seq methods. (e) Genome view of MACS peaks from ChIP-seq data of this study and of the study by Lien et al.23. Chr, chromosome number. Note that large-scale enrichment patterns across the genome are similar between the two studies, as expected. H3K27me3 shows visible reduction in overall signal in LC-HFSCs. (f) Genome-wide view of H3K9me3 (K9) ChIP-seq peaks in different sorted populations. Chr, chromosome number. Notice a dramatic reduction in the overall signal in LC-HFSCs.

Mentions:
To examine genome-wide distribution and levels of DNA-bound methylated histone H3 K4/K9/K27me3, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq). We used comparable number of sorted CD34+/α6-integrin+ EA-HFSCs (PD22–25) and LC-HFSCs (PD38–44; Fig. 2a,b). We also sorted and analysed non-HFSCs (nEA and nLC) counterparts as CD34−/α6-integrin+. Using IgG as background for normalization, our data revealed good correlation between experiments and enrichments in specific functional genomic regions, such as promoters, introns and repetitive regions, as expected (Supplementary Fig. 2a,b). We compared our data with a previous ChIP-seq study of H3K4me3 and H3K27me3 (H3K9me3 was not analysed) by Lien et al.23, done at Mid/late Anagen (MA-HFSCs) and Late Telogen (LT-HFSCs; Fig. 2a–e). The overall genome-wide distribution for the marks was similar in the two studies (Fig. 2d,e), however, our data uniquely revealed fewer ChIP-seq peaks in LC-HFSCs when compared with EA-HFSCs (Fig. 2c and Supplementary Fig. 2c). Close examination of ChIP-seq data distribution across the genome showed that for H3K27me3 and especially for H3K9me3 not only the total number of peaks but also the height was dramatically decreased in LC-HFSCs (Fig. 2e,f, arrows). In case of H3K4me3, the number of peaks were marginally decreased in LC-HFSCs relative to the other populations (Fig. 2c,e), which prompted us to examine the ChIP-seq signals in a manner that would allow more quantitative examination of signal at discrete chromosomal loci.